Hi, If I understood your question, do you want to know how can you start a simulation? So, if I'm correct I recommend this link http://www.gromacs.org/WIKI-import/Main_Page/Beginners to you. In this link, there is flowsheet file which is the flowchart to Gromacs simulation.
Answered your question a little more specific, although basically, after you get the pdb file, you need to run the pdb2gmx program. The link above explains more details about it. I hope that this email helped you. Cheers, -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 On Tue, Jul 21, 2009 at 4:52 PM, Jamie Seyed <[email protected]> wrote: > Hi, > > I have a basic question (since I am new). For starting any simulation as I > understand, is to find a .pdb or .gor file. Pdb files for proteins are > already there, but for a new system what is the easiest and quick way to > find it (which software etc). What about .gro files????? > > > > I appreciate your help for solve my basic problems. > > Thanks, Jamie > > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
_______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
